Hi,

I' am running galaxy locally and I have installed Bismark and its
dependencies from the Galaxy main tool shed. I receive multiple errors when
using a small test dataset.

(1) My first error occurs when I try running Bismark bisulfite mapper
(bowtie2):


Error indexing reference sequence
/bin/sh: /Users/charlesmurphy/Desktop/Research/tools/galaxy/shed_tools/
toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark/183de9d00131/bismark/bismark_genome_preparation:
No such file or directory


Which I can fix by editing the env.sh file in the dependencies directory. I
change:

SCRIPT_PATH=/Users/charlesmurphy/Desktop/Research/tools/galaxy/shed_tools/
toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark/183de9d00131/bismark;


To:

SCRIPT_PATH=/Users/charlesmurphy/Desktop/Research/tools/galaxy/shed_tools/
toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark/183
de9d00131/bismark/bismark_wrapper;


(2) My second error occurs when I try running Bismark methylation extractor:


usage: bismark_methylation_extractor.py [-h] [--infile INFILE]
[--single-end]
[--paired-end]
[--report-file REPORT_FILE]
[--comprehensive] [--merge-non-cpg]
[--no-overlap] [--compress COMPRESS]
[--ignore-bps IGNORE_BPS]
[--cpg_ot CPG_OT] [--chg_ot CHG_OT]
[--chh_ot CHH_OT]
[--cpg_ctot CPG_CTOT]
[--chg_ctot CHG_CTOT]
[--chh_ctot CHH_CTOT]
[--cpg_ob CPG_OB]
 [--chg_ob CHG_OB]
[--chh_ob CHH_OB]
[--cpg_ctob CPG_CTOB]
[--chg_ctob CHG_CTOB]
[--chh_ctob CHH_CTOB]
[--cpg_context CPG_CONTEXT]
[--chg_context CHG_CONTEXT]
[--chh_context CHH_CONTEXT]
[--non_cpg_context NON_CPG_CONTEXT]
[--non_cpg_context_ot NON_CPG_CONTEXT_OT]
[--non_cpg_context_ctot NON_CPG_CONTEXT_CTOT]
[--non_cpg_context_ob NON_CPG_CONTEXT_OB]
[--non_cpg_context_ctob NON_CPG_CONTEXT_CTOB]
bismark_methylation_extractor.py: error: unrecognized arguments:
--bismark_path
/Users/charlesmurphy/Desktop/Research/tools/galaxy/shed_tools/
toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark/183de9d00131/bismark


Seems to me the python wrapper lacks the code to tell galaxy where the
bismark_methylation_extractor executable is. I can go around the error by
 editing bismark_methylation_extractor.py. I add the following line:
parser.add_argument( '--bismark_path' )

Then on line 72 I change:

cmd = 'bismark_methylation_extractor --no_header -o %s %s %s'


To:

cmd = args.bismark_path + '/bismark_methylation_extractor --no_header -o %s
%s %s'



I suspect I' am not doing something correctly. Let me know if anything is
unclear or if you need more information. Thanks for any help!

Charlie
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